Preparing the images

All the software in the QUINT workflow have requirements for the input images:

  • The file naming convention applies to all the software. It is recommended to change the file names as the first step in the QUINT workflow. This ensures that the files are compatible with QuickNII and VisuAlign, and that the output files of QuickNII, VisuAlign and ilastik are directly compatible with Nutil.

  • As the image size requirements for QuickNII and Ilastik differ, it is recommended to generate two image series that comply with their respective requirements.


The Nutil software can be used to prepare the images since it supports image transformations (downscaling, rotation, mirroring), file renaming and file format conversion. Alternative software such as FIJI or Adobe Photoshop can also be used.

QUINT naming convention

  • Add a unique ID to each image that reflects the serial order and spacing of the sections.

  • The format is: _sXXX with XXX representing the section number (not restricted to three digits).

  • Do not use periods/full stops “.” or spaces within the file name.

For example, for consecutive sections: _s0001, _s0002, _s0003



Nutil Quantifier uses the _sXXX naming convention to match up corresponding atlas maps, segmentations and info in the XML/JSON file from QuickNII/VisuAlign. While not recommended, it is possible to bypass the naming convention using Regular Expressions (RegExp) as long as there is a consistent naming convention across the files. For more information see the “Help” button in the Nutil GUI or contact user support.